FOCUS

Brenton Brooks

Effect of different dwarfing genes on wheat yield traits

I have been an RPO at CSIRO for the last 10 years. I was involved in several projects with the objective of achieving higher yields in wheat through transferring desirable phenotypic or physiological traits. My current project is examining the impact of transferring chromosomes from rye into wheat to determine which characteristics can contribute to increased yield. My daily routine usually involves nurturing my plants in the glasshouse, or monitoring how they survive in the paddock. Hail and covid have therefore been destructive to project goals in 2020! My background is ‘classical’ plant breeding and I have worked as a breeder on a number of crops in the last 30 years ranging from wheat to cotton. This has been at government organisations and an international breeding company. The cotton company bred coventional and transgenic varieties. The San Remo pasta you eat is likely one of my durum varieties or their derivatives. Before I attended Data School FOCUS I was an R raw recruit. My data collection revolved around manhandling Excel.

Cathrine H Ingvordsen

Weed-Competitive Wheat

Hi, welcome to my Data School Final Project! I joined CSIRO in 2015 leaving Denmark for this great opportunity to work on agriculture in a country with tight link between growers and science and an agricultural sector sustainable without heavy EU subsidies. Before joining Data School my R experience was adopting colleagues scripts and running them on my own data - once figuring out how to load data from another source. Experiencing even more of the power R has on offer in Data School, I’m now determined to find the time to free myself from excel and the errors that can sneak in when I combine field measurements from different sheets - the errors that are complicated or impossible to back track - and make awesome figures.

Elaheh Arjomand

Improved Approaches to Long-Term Monitoring of Decommissioned Onshore Gas Wells in the Northern Territory

I am Elaheh Arjomand and I am doing a Post-doc fellowship on the subject of wellbore integrity and monitoring wells after being decommissioned. I completed my Ph.D. studying the integrity of the cement sheath in petroleum wells after being subjected to pressure and temperature variations at the University of Adelaide in 2018.

Elise-Andree Guerette

Evaluation of high-precision analytical techniques for measuring atmospheric nitrous oxide (N2O)

I am an Atmospheric Chemist who has recently joined the Major Greenhouse Gases team (GASLAB) at the Aspendale, VIC site. https://research.csiro.au/acc/capabilities/gaslab/ I started using R as part of my PhD and I was quickly hooked. Coding gives me both extreme joy and deep frustration, depending on whether my code works :) I used R throughout my postdoc and I am now keen to use my R skills in my new role.

Felicity McEnnulty

Monitoring endangered Spotted Handfish populations

I have a background in taxonomic identification of marine invertebrates and plankton. This requires working with data sets of species data and associated environmental data, spatial details and imagery. I have been involved in fieldwork using SCUBA diving to survey for introduced marine pests in Australian ports and to conduct underwater visual counts for species monitoring. I have used Excel, Access and SQL databases to manage data and have some experience in coding using Oracle to manage data and and R to produce graphs.

Gavin Hunter

Preliminary investigations into the population genetics of sea spurge (Euphorbia paralias) in Australia

I am a research scientist in the Temperate Weeds research group of the Managing Invasive Species and Diseases (MISD) research programme of Health and Biosecurity. I am a plant pathoglogist and use classical and DNA-based molecular techniques to investigate the interaction of fungal plant pathogens and their plant hosts. My daily work pattern invovles experiments undertaken in the laboratory, glasshouse and quarantine facilities. I had no previous programming skills before Data School but was always very interested in learning programming to broaden my analytical skill set.

Geetha Perera

Screening GM canola for tolerance to aluminium

I am Geetha Perera, a Research Technician with Agriculture and Food based in Canberra. At present I am a part of the Soil Constraint research team in the Crops Program. I had no experience in R before Data School, tried to self-learn but never happened. I have been using Excel extensively to record, summarise and visualise data mostly using bar graphs. My main aim in Data School FOCUS was to learn coding with R to replace the repetitive steps that I follow when working with data sets in Excel.

Jose Barrero

Transcriptomic analysis of high-oil transgenic cowpea

My name is Jose Barrero and I am a Research Scientist in Agriculture and Food. Although I have worked mainly with cereals in the past I recently started leading the Cowpea Team in Black Mountain. I have not done any coding before but I generate large datasets that need complex analysis, so that is why I decided to learn a bit of R and to come to Data School as part of my Julius Career Award activities.

Karen Aitken

Sequencing the complex polyploid sugarcane genome

I am a Principal Research Scientist in Agriculture and Food and my main interest is in understanding how polyploidy impacts crop genetic improvement. Before Data School I used SAS or GenStat for statistical analysis and for generating graphs either Excel or SigmaPlot. I joined Data School to learn how to create reproducible graphs from large sequence data sets. I did not have any previous experience using R language before Data School.

Nicole Murphy

Sustainable livelihoods in Torres Strait

Most of my work is in Torres Strait in collaboration with Traditional Owners, with a focus on stock assessment and harvest strategies for their hand collectable fisheries. I have spent a lot of time underwater collecting data and I now spend a lot of time with data outputs and analyses. I never used code before data school.

Ram Ghimire

Analysing biomass and yield of two contrasting leaf architectures of wheat

My name is Ram Ghimire, currently working as a Research Projects Officer in wheat leaf architecture and yield project. I have been working with data in crop physiology & agronomy for many years but have had no experience in R. Most of my data manipulation and visualisation are done in excel. I came to know about Data School from colleagues and got opportunity to join this year. Before joining Data School, I was used to spending a lot of time working with data mostly in excel spreadsheets. Now, I am delighted to see how amazing R can be for processing and visualisation of the field and laboratory data that I collect every year.

Sam Periyannan

Genetic analysis of stem rust disease resistance in wheat

With the background in genetics, plant breeding and crop pathology, I am currently working as a Scientist at the Crop Immunity group of Traits program of CSIRO Agriculture and Food business unit. As the pathogen causing rust disease of wheat evolves frequently overcoming resistance genes deployed in commercial cultivars, my role at CSIRO is to screen germplasm and wild relatives of cultivated wheat for novel resistance. Through genetic characterisation we identify markers linked to the new resistance thereby enabling rapid breeding of the identified resistance into elite wheat cultivars through marker assisted gene selection.

Shirleen Prasad

Genetics of stress- & domestication-related traits in Bactrocera tryoni

My name is Shirleen Prasad. I am a 3rd year Macquarie University PhD student based at CSIRO. My PhD project investigates the genetic basis of reduced stress resistance in domesticated Queensland fruit flies (Q-fly), Bactrocera tryoni. Before joining Data School, I mostly used excel for data analysis and could only perform basic statistical analysis in R. Gaining competence in R through this course has given me confidence in using R independently.

Sophia Escobar-Correas

Finding gluten proteins in cereal grains

Hello! My name is Sophia, I am a molecular biologist working in proteomics, currently a Postdoctoral Fellow. Before Data School, I coded using Macro (Excel). I used to spend a lot of time cleaning and tidying protein data; I always felt like I could do it faster if I had programming skills. These weeks learning R have changed my daily work. The skills I have obtained have allowed me to fast track the ordinary and focus on new perspectives of my research.

Tina Rathjen

Investigating flowering time in wheat under controlled environment conditions

I have been working as a molecular biologist for over 25 years on both animal and plant systems. The last 10 years I have worked at CSIRO and have been involved with several projects investigating different aspects of wheat physiology and growth. This has included carrying out laboratory, glasshouse and field experiments and previously data generated has been entered and analysed using Excel. Prior to Data School I did not know how to code or use R. Data School FOCUS has opened my eyes to a whole new world of data analysis and I hope to use this as a starting point to learn and apply new and exciting methodologies.

Trijntje Hughes

Summer is coming to OzWheat

I joined CSIRO over twenty years ago and have worked on many different projects mostly in wheat and barley. I love working in the laboratory combined with field and glasshouse work. My work involves varied aspects of seed biology, including seed dormancy, seed composition and environmental stresses. Before data school I would enter data either in FieldPrime or Excel and all my data analyses and visualisation was done in Excel. I had no experience writing code at all.

Tristan Louth-Robins

Project Support Centre Monthly Reporting (Draft)

I joined CSIRO in 2009 and worked in the Contract Administration Centre until 2014. Since then, I’ve covered a variety of roles supporting Project Support, In-Business Finance, Research Office and currently the Project Support Centre (Corporate Finance.) Prior to commencing Data School I could code in HTML and a bit of C, but its applications were largely restricted to extra-curricular activities away from CSIRO. Learning R and aspect of Data Management appealed to me as an attractive and valuable skill that could be applied in practice for the purposes of reporting, file management systems and general compliance activities.